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<li><a href="./">Snakemake book</a></li>

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<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Prerequisites</a></li>
<li class="chapter" data-level="2" data-path="introduction.html"><a href="introduction.html"><i class="fa fa-check"></i><b>2</b> Introduction</a><ul>
<li class="chapter" data-level="2.1" data-path="introduction.html"><a href="introduction.html#ratinale"><i class="fa fa-check"></i><b>2.1</b> Ratinale</a><ul>
<li class="chapter" data-level="2.1.1" data-path="introduction.html"><a href="introduction.html#what-is-reproducibility"><i class="fa fa-check"></i><b>2.1.1</b> what is reproducibility?</a></li>
<li class="chapter" data-level="2.1.2" data-path="introduction.html"><a href="introduction.html#what-is-reproducibility-really"><i class="fa fa-check"></i><b>2.1.2</b> what is reproducibility, really?</a></li>
<li class="chapter" data-level="2.1.3" data-path="introduction.html"><a href="introduction.html#why-snakemake"><i class="fa fa-check"></i><b>2.1.3</b> Why Snakemake?</a></li>
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<li class="chapter" data-level="2.3" data-path="introduction.html"><a href="introduction.html#install-software-using-conda"><i class="fa fa-check"></i><b>2.3</b> Install software using <code>conda</code></a></li>
<li class="chapter" data-level="2.4" data-path="introduction.html"><a href="introduction.html#backup-a-environment"><i class="fa fa-check"></i><b>2.4</b> Backup a environment</a></li>
<li class="chapter" data-level="2.5" data-path="introduction.html"><a href="introduction.html#whats-it-look-like"><i class="fa fa-check"></i><b>2.5</b> What’s it look like?</a></li>
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<li class="chapter" data-level="2.7" data-path="introduction.html"><a href="introduction.html#what-does-the-worflow-look-like"><i class="fa fa-check"></i><b>2.7</b> What does the worflow look like?</a></li>
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<li class="chapter" data-level="7" data-path="paired-samples-for-snakemake.html"><a href="paired-samples-for-snakemake.html"><i class="fa fa-check"></i><b>7</b> Paired samples for snakemake</a><ul>
<li class="chapter" data-level="7.1" data-path="paired-samples-for-snakemake.html"><a href="paired-samples-for-snakemake.html#convert-dictionary-content-to-wildcards"><i class="fa fa-check"></i><b>7.1</b> Convert dictionary content to <code>wildcards</code></a></li>
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<li class="chapter" data-level="9" data-path="workflow-of-wgbs-data-analysis.html"><a href="workflow-of-wgbs-data-analysis.html"><i class="fa fa-check"></i><b>9</b> Workflow of WGBS data analysis</a></li>
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<h1 class="title">Reproducible and scalable workflows with Snakemake</h1>
<h4 class="date"><em>2019-03-12</em></h4>
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<div id="prerequisites" class="section level1">
<h1><span class="header-section-number">Chapter 1</span> Prerequisites</h1>
<p>This is a book written for the reseasrchers who want to learn how to use Snakemake to build repruducible and scalable workflows. We assume the readers have already been familiar with NGS data analysis. For example, a tipycal workflow of RNA-seq data includes quality control of the reads, read alignment, read count extraction, DEG detection, GO and KEGG enrichment analysis.</p>

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